DNA Methylation as a Biomarker of Gestational SARS-CoV-2 Exposure: Differential Methylation Patterns in Placental and Cord Blood Tissues Model Third Trimester COVID-19

Background The placental and fetal epigenome is highly sensitive to physiological and environmental stressors, including infection, inflammation, and metabolic disruption. Altered DNA methylation patterns have been reported in association with a range of prenatal exposures, particularly maternal infection. The COVID-19 pandemic has introduced a large population of pregnancies exposed to viral infection in utero, creating a unique opportunity to study the epigenetic effects of prenatal SARS-CoV-2 exposure. While clinical outcomes of COVID-19 during pregnancy have been increasingly characterized, little is known about how SARS-CoV-2 interacts with the placental or cord blood epigenomes. Given the essential role of DNA methylation in placentation and its broader regulation of gestational health, examining these epigenomic signatures may reveal novel, clinically relevant insights into the effects of prenatal SARS-CoV-2 infection. Results No significant global differences in DNA methylation were observed between COVID-19 and Control groups within placental or cord blood tissues. However, regional analysis identified 58 significant differentially methylated regions (DMRs): 20 in maternal surface placental tissue, 36 in fetal surface placental tissue, and 2 in cord blood. DMRs in both placental surfaces were predominantly hypermethylated in SARS-CoV-2-exposed samples, whereas cord blood regions showed the opposite trend. Reactome pathway analysis of these regions in a tissue specific manner highlighted common enrichment of inflammatory signaling, metabolite processing, redox homeostasis, and neuronal signaling pathways. Subsequent machine learning models revealed predictive relationships between CpG-level methylation and COVID-19 status, identifying candidate biomarkers with potential clinical utility. These combined findings provide preliminary evidence that gestational SARS-CoV-2 infection is correlated with epigenetic alterations in placental and cord blood tissues in a predictable manner. Conclusion These data suggest that third-trimester SARS-CoV-2 exposure is associated with regional, tissue-specific DNA methylation changes in both placental and cord blood tissues. Functional pathway analysis identified these changes in methylation occurred at loci associated with oxidative stress regulation, metabolite processing, and neurodevelopmental signaling. Together, these results suggest that gestational SARS-CoV-2 infection may create epigenetic vulnerabilities with potential implications for offspring health. Further investigation in larger, longitudinal cohorts is needed to validate these findings and clarify their clinical significance.